In Modern Warfare 2, Ghost takes up Gaz's position from the first game, right down to sharing a voice actor. People originally even suspected they were one and the same character. This was later disproven in canon.
Colt from Monster Rancher 2 can be resumed as a 12 year old Holly with a tomboy hairstyle.
Also from Monster Rancher 2 is the Zuum, who is similar to the Dino from the first game. If you were to use the Slate command to import your Dino, it will be converted into a Zuum.
Tekken series: Roger Jr. (actually the unnamed mother) replaces Roger. Hwoarang replaces Baek (who then returns in Tekken 5 alongside his student). Jin Kazama replaces his father Kazuya (who then returns, Jin getting a different fighting style). Combot replacing Mokujin for Tekken 4. Devil Jin replacing Devil Kazuya and Angel (debatable; Devil Kazuya also functions as an alternate stance for Kazuya in Tag 2). Asuka replacing Jun Kazama. Christie replacing Eddy (who fully returned in Tekken 5; in 4 he was an alternate costume for Christie). Julia Chang replacing her foster mother Michelle Chang. Forrest Law replacing his father Marshall Law (who then re-replaces his son in the next game, Tekken 4). Each Jack-bot is the newest model (though apparently with the same mind transferred over). King dies before Tekken 3, and Armor King is killed before Tekken 4. Both Kings are replaced by their younger followers, and even the names remain unchanged. Even Kuma that appears in Tekken and T2 dies of old age and is replaced by its pretty much identical child in Tekken 3. In general, many Tekken character replacements are so similar that if you are not familiar with storyline details, you won't even know someone is not the same as the original.
Both Tag Tournament titles thrive on this trope by reunitingthe majority of the collective roster across all preceding games, thus allowing the originals and their newer counterparts to fight side-by-side. Even stranger is the fact that certain older veterans have their ages frozen at/reversed to that of their last canonical appearance yet still interact with their successors as if they were their actual ages in the current storyline (see: Jun and Jin, Michelle and Julia).
In Suikoden II we have Boris Wizen, who shares the Tengou Star with his father Ridley Wizen and will take his place if he dies in the Dunan Unification War. The player can indirectly decide who (s)he wants to keep: When Nanami asks you to run away in Tinto you can decide whether or not you want to do it. If you do, Ridley will be killed as a result and you will also see a few additional cutscenes, including the introduction of the new Kobold General. The only differences here are the looks and personalities.
At the end of the GBA version of the first Ace Attorney game, Phoenix's assistant Maya leaves to undergo spiritual medium training; she returns in the next game. When a DS remake of the first game was released, they added an extra case to it — but they couldn't bring Maya back, as one of the cases in the second game revolved around her reunion with Phoenix. So a new character, Ema Skye, became Phoenix's assistant for that one case. When the fourth game changed the entire cast (including Phoenix), Ema replaced Dick Gumshoe as the police detective who is routinely run into and switches between the main character's foil and friend.
This has led to a series of recurring archetypes, though no two characters feel truly the same. Phoenix's successor Apollo is also a snarky, put-upon lawyer constantly at the mercy of strange witnesses. Apollo is much snarkier and more sensible, though is flustered more easily. When playing as Phoenix in the fifth game, Apollo is generally a lot more cheerful than when playing as him.
Maya has also been replaced by Phoenix's adopted daughter Trucy, who is just as cheerful but more mature and not as mischevious than Maya.
When Edgeworth got his own spinoff, he picked up a Genki Girl assistant with a mysterious yet highly relevant past in the form of Kay Faraday.
The fifth game gives us Athena Cykes, a rookie attorney whose courtroom style fits early Phoenix Wright to a T, while her personality is much closer to the Genki Girl assistant role.
Phoenix himself is a Suspiciously Similar Substitute to the young version of his mentor Mia Fey, and the older Phoenix from Apollo's game is rather similar to the older Mia from Phoenix's games.
After Miles Edgeworth, a prickly, win-at-any-costs prosecutor with a tie to one of the heroes in the first game, he's replaced by his adoptive sister Franziska in the second game and the coffee-guzzling Godot in the third. Both are rather similar in temperament and tactics. Apollo's rival Klavier is the exception, as he's actually as laidback and nice as he seems, and has no beef with Apollo.
In the fifth game things are back to form with prosecutor Simon Blackquill and detective Bobby Fulbright.
The series-opening prosecutor Winston Payne has been replaced by his brother Gaspen Payne and his English counterpart Prosecutor Flynch in Professor Layton vs. Ace Attorney.
In the second Ace Attorney Investigations game, you meet a reporter called Mikiko Hayami in the first case who seems to be this for Lotta Hart. However, Lotta herself later shows up, and it turns out the two reporters know each other.
Sonic Adventure introduced us to Gamma, a well-armed red and white humanoid "E-Series" Greek-letter-named robot created by Eggman, who over the course of the game decided to turn against Eggman. At the end of the game, Gamma died. A few years later, Sonic Heroes brought back a whole bunch of characters, adding no new ones... except Omega, a well-armed red and white humanoid E-Series Greek-letter-named robot created by Eggman who had decided to turn against Eggman. Hmm... On the other hand, they are radically different in terms of personality: while Gamma was a conflicted and ultimately tragic character, Omega is a borderline mechanical psychopath that wants to obliterate his former master (and everything he built) and then ultimately take over. And he talks like aDalek.
Sonic Battle has a different Gamma substitute, "Chaos Gamma" — a mass-produced model based on Gamma without enough intelligence to rebel against its master.
The main reason is that Raidou has the Pierce skill, an absolute necessity if you want to face the True Final Boss (and honestly, at the point you recruit Raidou/Dante, that's the only thing left for you to do). Dante was cool, but his lack of Pierce, inability to get Pierce (because you couldn't fuse him with anything) and permanent consumption of one of your party slots reduced him to Awesome, but Impractical.
The first print versions of the NES entry starred Mike Tyson as its final opponent. Eventually Nintendo's license to use Tyson's likeness in a game expired (and since he was no longer the undefeated world heavyweight champion, renewing the license was less desirable...and would become even less so when Tyson was convicted of rape a year later), so the 1990 reissue substituted Tyson with the fictional Mr. Dream, a white boxer who's exactly the same (he even has the same end-of-round quotes).
The Wii installment has Disco Kid, originally an updated version of Kid Quick from the first arcade game. As the staff updated his design, he changed so radically that they decided it would be easier to make a different character out of him. His files on the disc are still labeled "kid_quick."
Piston Honda from the NES version was essentially a substitute for Piston Hurricane from the first arcade game. The SNES game brought back Piston Hurricane (along with other previously arcade-exclusive opponents), only to bring back Piston Honda (under the guise of Piston Hondo) in the Wii installment.
Kratos and Zelos in Tales of Symphonia, with the latter replacing the former. They are almost identical in regards to combat: Kratos has slightly better stats, but Zelos has slightly different attack animations that makes him a bit better at using combos, and their only real differences are titles and a single move they can learn.note Kratos can learn Judgment in the original NTSC version, but in PAL and HD re-releases, Zelos can learn also Judgment plus the Divine Judgment Overdrive. However, this is averted with their personalities: Kratos is a StoicMercenary who turns out to be an Enigmatic Minion for the Big Bad and Zelos is a comical on the outsideClassical Anti-Hero and The Casanova, who seems to need babysitting a lot.
When Pey'j gets in trouble in Beyond Good & Evil, his place in the party is taken by Double H, the soldier. Again, they have completely different characters, but effectively the same function, and only show up together for a brief time in The Very Definitely Final Dungeon.
In the original Snatcher, the engineer Harry Benson dies. When it was reinvented as an RPG in SD Snatcher, Harry provides all the weapons and ammunition to Gillian. To make sure the player could still buy weapons and bullets after Harry's death, a new character, Geoff, was added as Harry's apprentice. After Harry dies, Geoff takes over the weapons store.
In Pikmin 2, when your main Sidekick Louie goes missing after you complete the game's main mission, he gets replaced with the President of the Hocotate Shipping Company, who remains with you even after you rescue Louie.
The jump from Nintendo GameCube to Wii caused a few problems with the Naruto games, so some characters were left out of Clash of Ninja Revolution. Zabuza's replacement was the shark-swordsman Kisame Hoshigaki. This was probably for the better. In Japan, meanwhile, Sasuke was replaced by his brother Itachi.
In the Soulcalibur games, Maxi replaces Li Long (from the prequel, Soul Edge) as the game's nunchaku user, after Li's defeat at the hands of Cervantes. Li has only returned as a bonus character in Soulcalibur III.
Cassandra replaces Sophitia in Soulcalibur II (though Sophitia can be unlocked in the home versions), and Yun-seong replaces Hwang in spirit and general appearance, although doesn't have exactly the same moves. It's also notable that in this game the unlockable character Assassin DOES have the same moves as Hwang, and his fellow unlockable Berserker has those of Rock, however neither of these characters are canon to the story and so were probably included due to fanservice (and their use in Story mode). Kilik replaces Seong Mi-na officially although both characters are still available, and his moves have become more unique by III.
In the Korean versions, Misturugi was replaced by Arthur, a Caucasian samurai with the same moveset. He was then available in Soulcalibur III as a bonus character.
Olcadan in Soulcalibur III, as a replacement for Charade who was a replacement for Edge Master. Bonus points: each one is a Ditto Fighter, so they already act like other characters.
It's worth mentioning that when Soulcalibur was in development, Namco wished to completely overhaul the roster and only include a couple of characters from Soul Edge/Blade. Eventually, however, all the characters barring Li Long and Han Myong (Seong Mi-na's father) returned for the home version (Soul Edge was renamed Inferno). Li Long returned later anyway. As a result some of the characters in Soulcalibur start off closer to clone characters than they are originally (Kilik, Astaroth, etc.) but end up becoming different later on.
Soulcalibur V takes place about 17 years after IV, and has some of the main cast replaced by new characters, though each is given a sufficient explanation. Natsu replaces Taki, though she is Taki's apprentice. Yan Leixia is Xianghua's daughter. Even though she has sufficient reason to be a fighter in the game, there's no explanation given as to why Xianghua herself isn't playable. Xiba has Kilik's moveset, and the backstory reveals that he is the estranged son of Kilik and Xianghua, and half-brother of Leixia. Patroklos Alexander and Pyrrha Alexandra are the children of Sophitia, who sacrificed her life to save Pyrrha's when she was a child. Both characters have similar fighting styles to both Sophitia and Cassandra, and Pyrrha later becomes a direct copy of Sophitia's moveset later in the storyline. Cassandra herself isn't in the game because she was sucked into Astral Chaos after she was knocked unconscious by her sister in IV. Edge Master comes back from the original Soulcalibur, and Olcadan and Charade are nowhere to be found. He still uses every character's moveset. Kilik himself is still around, but he's an SNK Boss-turned-Secret Character who mimics all the male character's movesets, much like Edge Master.
Vice Project Doom: Your character's informant that they talk to at the end of each stage will leave partially through the game. A stand-in will fill in for her. You find out where your original informant went as the game progresses.
Each major entry in the Ape Escape series replaces the previous Kid Hero with a new one. In Ape Escape 2, Spike gets replaced by his cousin Jimmy (though he can be unlocked as a secret character). Jimmy gets replaced by Kei and Yumi in Ape Escape 3. Meanwhile, their aunt Aki replaces both the Professor and Natalie in their roles. Dr. Tomoki takes over Jake's role as Specter's dragon. However, all of them have distinct personalities.
Due to him being an obvious ripoff of Tetsuo Shima from the AKIRA manga (or because SNK just don't plain like him), K9999 from The King of Fighters 2001 was kicked out in the Updated Re-release of KOF 2002 (Unlimited Match) and replaced by "Nameless," whose fighting style is fundamentally identical to K9999's as well as his backstory, being cloned from Kyo and K'. While K9999 is a complete jerk, Nameless' story makes him rather sympathetic (thanks to his Morality Pet Isolde).
Vice and Mature's original role as Rugal's secretaries was taken over by Aya and Hermoine in The King of Fighters '98.
In Street Fighter Alpha, Guile, the Air Force lieutenant seeking revenge for his dead comrade, is replaced with Charlie, another member of the Air Force. Though in-universe, it's the other way around; Alpha is a prequel to Street Fighter II, so it would thus make Guile a replacement for Charlie (and, in fact, Charlie is the "dead comarade" Guile is seeking to avenge in SFII).
Remy from Street Fighter III is a much less confusing example, using Guile/Charlie's moves but coming after them both in and out of universe.
Also from Street Fighter III we have Urien, brother of Final Boss Gill. Visually, the only difference between the two are their colors and heads, and while their moves have enough difference in them to make them unique characters. it's very obvious that Urien was created to be a toned-down, playable, tournament legal Gill. Interestingly, the fact that he's an interesting character and an effective fighter in his own right has made him more popular than Gill, who has never been playable outside of console releases and has never been tournament legal.
In Marvel vs. Capcom, the developers couldn't use Iron Man due to licensing issues, despite being previously featured in Marvel Super Heroes, so they simply recolored his sprite from that game to make War Machine. When Capcom was able to use Iron Man again for Marvel vs. Capcom 2: New Age Of Heroes, they gave War Machine the moveset of his "Hyper War Machine" counterpart from the previous game in order to distinguish him from Iron Man, who used War Machine's regular moveset from the previous game (which in turn, was based on Iron Man's move set from Marvel Super Heroes).
The heroes of Golden Axe III, Kain Grinder and Sarah Barn, look and fight similarly to Ax Battler and Tyris Flare, respectively (to the point that the English manual for the Virtual Console version refers to them as such). Sarah even gets Tyris' repertoire of fire magic. Gilius Thunderhead is the only character from the previous installments to return in that game, though not as a playable character.
Blazing Sword'' — full circle, actually. Nils is the not so Spoony Bard in the introductory campaign, then he's replaced by Ninian, his sister. But then Ninian kicks the bucket, so Nils replaces her in the final battle.
From one game to the next half the cast will be this for the previous game. There's a set of archetypes that are well known in the fandom such as the two (occasionally three) cavaliers and the Jeigan.
Fire Emblem Fates has Luna, Lazward, and Odin based on Severa, Inigo and Owain from Fire Emblem Awakening. Subverted in that they actually are those three, or at least alternate versions of them from another world.
In the PSP Game Jeanne d'Arc, Liane is burned at the stake in Jeanne's place, and replaced by Cuisses, who is, thankfully, virtually the same. (Because Liane was probably one of your healers)
Pewee Piranha and Digga Legg from Super Mario Galaxy 2 are suspiciously similar substitutes to Dino Piranha and Megaleg from the original Super Mario Galaxy. The former is even found in the same general point in the game as the latter, and defeated in nearly the same way. Also, the Topmen from Galaxy are the same thing as the Bullies from Super Mario 64, both being enemies defeated by being pushed off the edge of the platform. They even both have nearly the same boss battles in the Mario Kart series!
The first two partners in Paper Mario: The Thousand-Year Door, Goombella and Koops, are similar at first to the first two in the original Paper Mario, Goombario and Kooper, having the same attacks and abilities- except upgraded. Also, unlike Kooper, Koops actually has a personality. After that though, the partners are all new, although Admiral Bobbery has the same abilities as Bombette (who is also a Bob-Omb) and Vivian's field ability is functionally identical to Bow's.
Peach is a substitute for Pauline, the damsel in Donkey Kong, and she's one of the few examples to overshadow her predecessor. When they brought back Pauline in Donkey Kong '94, they had to dye her hair color to brown to distinguish her. Some Japanese fans mistakenly believe the DK94 version of Pauline to be a different character from the Pauline in the original 1981 arcade game, due to Pauline originally being named Lady in Japan.
Foreman Spike from Wrecking Crew was Mario's original rival, an irritable tough guy with crazy facial hair and a grudge. He was essentially a prototype version of Wario and Waluigi; Mario Kart DS even lampshades this by having Waluigi's default kart, the Gold Mantis, be Spike's steamshovel.
In Yoshi's Island DS, about half the bosses and a good few of the levels are nearly the same thing as their equivalents from the first game. The Big Burt Bros are the most obvious; they're just two smaller versions of Burt the Bashful, killed the exact same way and found in a level with roughly the same layout. Others include Bungee Piranha (which is very much like Naval Piranha, complete with a castle designed like a sewer system) and Bowser himself, who acts as a near identical replacement to both Hookbill the Koopa and the giant version of his baby self.
In Donkey Kong 64, the playable characters Tiny and Chunky Kong are almost identical in form and function to Dixie and Kiddy Kong from Donkey Kong Country 2 and 3 respectively. The instruction booklet states they're the younger sister and older brother of the two. Tiny eventually grew out of this when she received an age-up.
from Pokémon Ruby and Sapphire onward, Pokémon games feature Pokémon that are somewhat similar (or substitutes) of already existing Mons. Example: Instead of Caterpie, Metapod, Butterfree, Weedle, Kakuna, and Beedrill as Bug-type Mons that evolve from worm-like creatures with a cocoon stage in the middle, we get Wurmple (essentially Weedle, with same stats and attacks) which can evolve into Silcoon, then Beautifly (similar to Butterfree) or Cascoon, then Dustox (a Poison-type like Beedrill, but a moth).
Also, Seviper replaces Ekans and Arbok in Hoenn games, due to the latter two not being native to Hoenn.
Most of the male protagonists are this to the original hero, Red. Ethan, Brendan, and Lucas take after his original design while Hilbert, Nate, and Calem take after his modern one. The latter two are also copies of Hilbert, most obviously with Nate. Rosa bears a strong resemblance to Hilda. Both protagonists of Pokémon Sun and Moon look like Calem and Serena from Pokémon X and Y.
And more obviously, each game features different monsters filling certain gameplay 'slots'; the Fire/Water/Grass starter trio, rodenty Normal-type and bird Flying-type Com Mons, and so on.
And every new generation introduces a new cute electric species with colored cheeks.
Also there's Team Magma/Aqua stealing Team Rocket's spot as the antagonistic gang... then Galactic in gen IV and Plasma in V. The fact they always carry the "Team" prefix (or the "Dan" suffix in Japanese) doesn't help to hide this trope's invocation.
While Final Fight 2, the straight-to-SNES sequel to Final Fight, kept Haggar from the original game, it also replaced Guy and Cody with Guy's sister-in-law Maki and South American swordsman Carlos respectively. While their techniques have many aesthetic differences from their predecessors (i.e.: Carlos uses his sword for his special attack instead of a spinning jump kick), they're the same and they even have the same abilities (Maki can do an off-the-wall jump kick, while Carlos can stab enemies with a knife).
Lampshaded in the intro of MegaRace 2. Lance tells his assistant, "You're fired," then turns to the camera and says, "Just kidding, folks. You'll be seeing Charlene, or somebody surprisingly similar, throughout the show. Believe me, you won't tell the difference. I won't, and I should know."
In Dead or Alive 2, Bayman from the original game was replaced by another character named Leon, who had the same moveset. When Bayman was brought back in later versions, he and Leon were given different movesets.
Dead Or Alive 4 had a Spartan, Nicole-458 as a guest character. While she doesn't appear in later games, Dead Or Alive 5 Ultimate has Rachel from Ninja Gaiden who has more than a few of Nicole's moves.
Contra: Hard Corps for the Sega Genesis substituted the traditional Contra heroes of Bill Rizer and Lance Bean with four new characters. Among the cast includes Sheena Etranzi (a female commando), Brad Fang (a cyborg werewolf), Browny (a tiny robot), and Ray Poward (a standard male commando). Guess which of these characters is most like Bill Rizer (hint: it's not the woman, the werewolf, nor the robot)...
According to Word of God, Roxas from Kingdom Hearts was made one of these on purpose in 358/2 days, due to worries that people might be uncomfortable playing through the whole game with a character who plays too differently from Sora. So his stats, abilities, and magical capabilities were Sora-fied. This, however, is justified, since Roxas and Sora are essentially the same person anyway.
Nu-13 was killed off at the end of BlazBlue: Calamity Trigger by falling into a dead time-stream. BlazBlue: Continuum Shift introduced Lambda-11, who re-uses Nu's sprites and rebalanced versions of Nu's moves. Justified because both characters are mass-produced robot clones.
Continuum Shift later reveals that Lambda-11 actually has Nu's soul. Expect this trope to happen again if a sequel to Continuum Shift is announced, because Lambda also dies in the end of Continuum Shift.
To our surprise, Blaz Blue Chrono Phantasma subverted this trope by bringing back Nu-13 exactly the way she was in Calamity Trigger. Unfortunately for those who liked Lambda-11's character development, thanks to Continuum Shift's True End, is null and void. Because you can hardly carry that kind of stuff onwards when you're a cyborg and your brain gets reset to factory settings thanks to being destroyed... And then self-regenerated. This later bit of information is yet to be explained properly...
And as of the recently announced Version 2.0, Lambda is returning to the game, alongside Nu. She will take Nu's Luna Form half and both will receive new abilities to make up for the ones they lost, effectively pushing Lambda out of this trope and into being a clone of Nu.
In Project Justice, Large and in Charge school principal Raizo doesn't make a playable appearance, the storyline explanation being that he was hospitalized thanks to an assassination attempt on his life. When that assassin (Kurow) becomes playable, his movelist is Raizo's own, with a few completely new moves thrown in to differentiate the two.
You'd think a white-haired and feral man-mountain and a gray-haired 15-year old with Freddy Krueger's gloves wouldn't be too similar. You'd be not-right.
The Legend of Dragoon replaces Lavitz with Albert after the former's death and also replaces Shana with Miranda later on. Functionally, they're almost identical, having the same additions and spells with a few minor traits. Although to some, Miranda is a Replacement Scrappy.
That would be because Miranda has nothing really unique about her compared to Shana sans her personality, which is rarely expressed or see after the conclusion of the Mille Saseau arc in the game. Albert, on the other hand, is a significant supporting character with a distinct personality. Lavitz's Additions have of the speed of a Mighty Glacier while Albert's Additions are more of a Lightning Bruiser type.
In Baldur's Gate 2, Imoen, a red haired human thief/mage is captured early in the game. Luckily, Nalia, a red haired human thief/mage is one of the first NPCs encountered afterwards.
Pash, it's not just appearance and class. The latter has the same cheerful personality and similar alignment as the former, allowing Imoen to become a much darker character.
In terms of party utility, Yoshimo also counts as Imoen's substitute. He is also a thief-type class, becomes available shortly before the need for replacement appears and right after he becomes unavailable, the original character returns.
Dragon Age: Origins – Awakening features a snarky, bitchy, forest-dwelling, human-hating mage as a party member. No, Morrigan doesn't make a comeback; it's only Velanna.
EarthBound has Ness, who is Ninten from the first game with a backpack; Paula, who is Ana with a different hair style; and Jeff, who is Lloyd with a school uniform. Somewhat done in MOTHER 3 with Lucas taking over Ninten and Ness's roles, except he looks completely different, but completely averted with Kumatora, who is completely unlike Paula and Ana, except for somewhat similar PSI.
In Mortal Kombat 4, Reiko replaced Noob Saibot early in development, although Noob could be found partially Dummied Out in the console versions. Kano was replaced by Jarek in the same game, who had mostly the same moves and fatalities, then Kano returned in Deadly Alliance, only to be killed off and replaced by Kobra in Deception.
Similarly, Robo from Chrono Trigger => Grobyc from Chrono Cross — they don't look nor sound anything alike, but fill the same character archetype (read "Grobyc" backward), complete with lack of magical ability — Robo is completely magic-inert (though lasers and tech-generated electricity count as Shadow attacks), while Grobyc can cast magic but sucks at it and has one of the weakest Element grids.
Between Resident Evil 1.5 and Resident Evil 2, Elza Walker, John, and Linda were redesigned into/replaced by Claire Redfield, Robert Kendo, and Ada Wong, respectively. The "Hooked Man" prototype of Resident Evil 4 had paranormally animated suits of armor, while the final version had Plagas-controlled armor suits, and Ashley replaced Sherry as the Damsel in Distress.
Mass Effect 2 can have this depending on the player's actions in Mass Effect. If Wrex survived the first game, he will appear on Tuchanka leading his clan. If he was killed, it will be his brother Wreav, offering the same quests and exposition (although his personality is notably different). Likewise, if you saved the colony of Zhu's Hope but let Shiala die, an unnamed human colonist will appear in her place on Illium to offer the same quest.
Because the Geth don't play nearly as big a role in Mass Effect 2—and they undergo Character Development to make them seem much less villainous—the various enemy factions' "mech" units end up filling their old roles as disposable robotic adversaries. The weak LOKI mechs are analogous to the basic Geth troopers, the quick quadrupedal FENRIR mechs are analogous to Geth Stalkers, and the giant lumbering YMIR mechs are analogous to Geth Primes.
In the third game, there are quite a few of these, since any or all of your squad can die in 2 if you're not careful. Mordin is replaced by another salarian named Padok Wiks (who appears regardless, but quickly vanishes if Mordin is still alive), Grunt is replaced by a generic krogan soldier, Miranda is replaced by her sister Oriana, Tali is replaced by Admiral Xen on the Dreadnought and Admiral Raan on Rannoch, and Legion is replaced by...a backup copy of itself (who doesn't have memory of Shepard). Garrus, Jacob, Jack, Zaeed, Kasumi, Samara, and Thane simply have their parts skipped if they died. Joker will even insist on referring to Padok as "Not-Mordin". In some of those cases, the outcomes of various situations will be different with the substitutes than with the originals, often to the player's detriment.
The most extreme example is the original Citadel Council. If left to die in Mass Effect 1, they are replaced in Mass Effect 3 by a "new" Council that uses slightly different models but mostly the same dialogue. Although, notably, the replacement salarian councilor is female, and the one time Udina calls them by their personal names — the only instance they're named in all three games — the names are different for the old and new Council. Notably, the replacement turian councillor, Quentius, is far less opposed towards the idea of the races uniting their forces rather than focusing on defending themselves compared to his predecessor, "Ah yes, Reapers" Sparatus.
Anarchy Reigns gives us the Black Baron, former grand champion of the Varrigan City DeathWatch. Oh wait, no, that's actually the Blacker Baron, a cyborg pimp who acts and fights just like the blackface battler.
Professor Layton and the Specter's Flute is a Prequel, and therefore set before Layton meets Inspector Chelmey or Don Paolo. So there's a different Scotland Yard inspector and deranged supervillain.
Rena Hayami, the protagonist of R: Racing Evolution, a simulation spinoff of the Ridge Racer series, bears a resemblance to Reiko Nagase from the main series.
Galuf from Final Fantasy V is replaced mid-game by his granddaughter Krile, who inherits all his experience, items and job mastery. Averted in all other Final Fantasy games.
In World of Warcraft, when the Zul'Aman instance was retooled from a 10-man Level 70 raid to a 5-man Level 85 Heroic dungeon, the final boss, Zul'Jin, being canonically dead as of Cataclysm, was replaced by Daakara the Invincible. While Zul'jin started as a troll, then turned into a bear, eagle, lynx and dragonhawk in turn each time players took off 20% health, Daakara started as a troll, then switched to either a bear then an eagle, or a lynx then a dragonhawk, with mostly similar mechanics to Zul'jin's versions of the forms.
In the Blackrock Depths instance, if players completed the quest to rescue Princess Moira from Dagran Thaurissan, she would be replaced by a Priestess of Thaurissan on subsequent encounters, who would also heal Dagran.
In the updated version of Scarlet Monastery for Mists of Pandaria, Renault Mograine, having been killed by the spirit of his father in the Ashbringer event is replaced by Scarlet Commander Durand as Whitemane's partner in the Dual Boss battle.
When Gat dies in the second mission of the third game, Shaundi, previously the Fun PersonifiedOne of the Boys character from the second game, becomes the boss's borderline psychotic ally while Pierce, formerly the Ambiguously GayButt Monkey, takes on Gat's role as the Boss's right hand man. While Pierce got to keep his personality, Shaundi had little to nothing of her former self left. Does it count as SSS if the replacement was an already existing character?
A recent trailer for Saints Row IV reveals Shaundi from Saints Row 2 and Shaundi from Saints Row the Third as being character in the game, so Shaundi from Saints Row the Third is actually a SSS for Gat personality wise, and a SSS for Shaundi from Saints Row 2 name wise.
This actually came back to bite SRW years later: Sunrise, the studio that owns Gundam, complained about the Huckebein seriesnote Never mind that it was created by Hajime Katoki, one of the better-known Gundam mecha designers. When Second Original Generations came around, an enemy character deliberately destroys the entire Huckebein line (which were all conveniently gathered in one place and vulnerable), and they're replaced by the Exbein, which is literally nothing but the old Huckebein Mk-III with a less Gundam-like face. After this incident, The Federation simply decides to stop making Huckebeins because... Because.
And then it comes full circle with the Exbein, in Original Generation 3, becoming the next step in the Huckebein development. After the Mk-III, not in spite of. This made anime continuity all but impossible for most writers out there.
In Rhythm Heaven, the Choir Boys from Glee Club were Ensemble Darkhorses, so for Rhythm Heaven Fever, the mascot Marshal was based on their design, with Cam and Miss Ribbon added to make the use of this trope less obvious.
In racing games developers typically substitute Porsche for RUF, due to Electronic Arts holding exclusive rights to the Porsche brand in videogames. RUF cars are tuned and rebadged Porsches (like what Shelby is to Ford), with more power and a slightly different bodykit, but effectively identical to a standard Porsche visually. If you see a RUF listed in a game's car lineup, it basically means there will be no Porsches in the game. The Forza Motorsport series featured Porsche in Forza 3, but when Forza 4 came around, Porsche was totally absent due to meddling from Electronic Arts, with only a trio of RUF 911s replacing the 20+ Porsches missing. An expansion pack was later released which re-added Porsche, though Porsches were not featured in any other DLC. When Forza Horizon came out, Porsche was, yet again, absent.
Meanwhile, something very much like Pyramid Head appears in Silent Hill: Homecoming, though it's unclear if this is actually Pyramid Head or something that looks like Pyramid Head, but has a different name.
The Walking Dead: Jane in Season 2 is this to Molly in Season 1. Both are tough female survivors with an inclination towards stealth and dirty fighting, both have a loner attitude brought on by losing younger sisters in tragic circumstances, both have extremely pragmatic and somewhat ruthless attitudes towards survival that raise more than a few eyebrows, and both only stay with the party for a while before leaving due to personal reasons, though Jane returns at the beginning of the final episode of the season and plays a major role in the ending.
In Time Crisis 2, Christie fills the role of the red-dressed Damsel in Distress Rachel from the first game, down to having the same voice actress, Lynn Harris.
Yosuke Hanamura from Persona 4 is this to Junpei Iori from Persona 3. They're both of the Magician Arcana, and both the first to join the protagonist's party. They also both transferred to the school the year prior, thus bond with the New Transfer Student protagonist because they know what it's like being the new guy. And finally, they both are a Loveable Sex Maniac, despite having a canon love interest who dies as part of the storyline.
From the same series, Yusuke Kitagawa from Persona5 is this to Jun Kurosu from Persona2. Yusuke's character design is basically a copy of Jun's, then both of them have been abandoned by their mothers, both of them are Sixth Ranger of the main party, and have great interest in beauty.
Party member Midea in Radia Senki Reimeihen has identical stats and techs to Saria, a prior party member who leaves after being revealed as The Mole. In fact, she joins with exactly as much experience as Saria had and with all of the techs Saria had learned.
Adeleine from Kirby is a complicated example. The character Ado only appears in Kirby's Dream Land 3. She has short hair and wears androgynous clothing so many fans mistook her for male (and in fact one of the arguments for Ado being different from Adeleine was "Ado isn't a girl"), though the manga and later a 20th anniversary game confirmed that she is female. Kirby 64: The Crystal Shards introduces Adeleine, who is near-identical to Ado in both design and role and has an extremely similar name. It's never been confirmed if "Ado" is Adeleine's nickname, a shortening due to the text box sizes in Dream Land 3, or whether they're separate individuals.
Golden Sun: The second game begins with the characters the previous game had been pursuing. While their personalities are different, their classes are functionally identical- Isaac and Felix are both Squires, Ivan and Sheba are both Seers. And in the third game, the tradition continues with Matthew and Tyrell, who take their respective fathers' classes (Isaac and Garet).